In March 1981, serving as an ad hoc Judge of the Supreme Court of Pakistan, he refused to take a fresh oath, under the Provisional Constitutional Order (PCO) promulgated by GeneralZia-ul-Haq along with Justice S. Anwarul Haq, Justice Maulvi Mushtaq Hussain and Justice Dorab Patel. The PCO not only negated the independence of the judiciary but also prolonged martial law by nullifying the effect of a judgement giving General Zia’s regime limited recognition.

Ebrahim served as the Governor of Sindh from 19 April, 1989 to 6 August, 1990. He was preceded by Justice (retd) Qadeeruddin Ahmed and succeeded by Mahmood A. Haroon.

Ebrahim established the Citizen Police Liaison Committee (CPLC) in 1989. The CPLC works in the mega city of Karachi and has immensely helped the common man in getting the First Information Report (FIR) registered if it is refused by police for some any reason.

Ebrahim heads the law firm of Fakhruddin G. Ebrahim & Company which was originally established in Bombay (now Mumbai, India). The firm shifted to Karachi in 1951. The firm is a regarded general legal practice.

Ebrahim has had long-standing ties with the Pakistan Cricket Board (PCB). In 1995, the PCB initiated an inquiry, under the chairmanship of Ebrahim, to look into allegations made by Australian players Shane Warne and Mark Waugh surrounding the First Test between Pakistan and Australia in Karachi in 1994 and the ODI in Rawalpindi. The Australian cricketers had accused Salim Malik of offering them bribes which they rejected. The inquiry was frustrated as the Australian players did not travel to Pakistan to give evidence, and thus the Inquiry had to rely on their statements together with the cross examination of Salim Malik. In October 1995, Ebrahim concluded the proceedings by saying "The allegations against Saleem (sic) Malik are not worthy of any credence and must be rejected as unfounded". In December 2006, Ebrahim also served as the Chairman of the Anti-doping Appeals Committee constituted by the PCB which acquitted Shoaib Akhtar and Mohammad Asif. Justice Ebrahim was in favour of the acquittal. Statement by Justice Ebrahim: "This appeal committee [therefore] holds that will not be deemed to have committed a doping offence," Ebrahim said. "The ban and punishment imposed by the earlier tribunal is hereby set aside as being contrary to the provision of laws."